van Helden J - Search Results

1

Ancestral state reconstruction of metabolic pathways across pangenome ensembles.

Psomopoulos FE, van Helden J, Médigue C, Chasapi A, Ouzounis CA. Psomopoulos FE, et al. Among authors: van helden j. Microb Genom. 2020 Nov;6(11):mgen000429. doi: 10.1099/mgen.0.000429. Microb Genom. 2020. PMID: 32924924 Free PMC article.

2

Transcriptional and epigenetic signatures of zygotic genome activation during early Drosophila embryogenesis.

Darbo E, Herrmann C, Lecuit T, Thieffry D, van Helden J. Darbo E, et al. Among authors: van helden j. BMC Genomics. 2013 Apr 5;14:226. doi: 10.1186/1471-2164-14-226. BMC Genomics. 2013. PMID: 23560912 Free PMC article.

3

Predicting metabolic pathways by sub-network extraction.

Faust K, van Helden J. Faust K, et al. Among authors: van helden j. Methods Mol Biol. 2012;804:107-30. doi: 10.1007/978-1-61779-361-5_7. Methods Mol Biol. 2012. PMID: 22144151

4

Prediction of metabolic pathways from genome-scale metabolic networks.

Faust K, Croes D, van Helden J. Faust K, et al. Among authors: van helden j. Biosystems. 2011 Aug;105(2):109-21. doi: 10.1016/j.biosystems.2011.05.004. Epub 2011 May 27. Biosystems. 2011. PMID: 21645586 Review.

5

[Tracing the origins of SARS-COV-2 in coronavirus phylogenies].

Sallard E, Halloy J, Casane D, van Helden J, Decroly É. Sallard E, et al. Among authors: van helden j. Med Sci (Paris). 2020 Aug-Sep;36(8-9):783-796. doi: 10.1051/medsci/2020123. Epub 2020 Aug 10. Med Sci (Paris). 2020. PMID: 32773024 Free article. French.

6

Pathway discovery in metabolic networks by subgraph extraction.

Faust K, Dupont P, Callut J, van Helden J. Faust K, et al. Among authors: van helden j. Bioinformatics. 2010 May 1;26(9):1211-8. doi: 10.1093/bioinformatics/btq105. Epub 2010 Mar 12. Bioinformatics. 2010. PMID: 20228128 Free PMC article.

7

The chromatin environment shapes DNA replication origin organization and defines origin classes.

Cayrou C, Ballester B, Peiffer I, Fenouil R, Coulombe P, Andrau JC, van Helden J, Méchali M. Cayrou C, et al. Among authors: van helden j. Genome Res. 2015 Dec;25(12):1873-85. doi: 10.1101/gr.192799.115. Epub 2015 Nov 11. Genome Res. 2015. PMID: 26560631 Free PMC article.

8

Integrating Bacterial ChIP-seq and RNA-seq Data With SnakeChunks.

Rioualen C, Charbonnier-Khamvongsa L, Collado-Vides J, van Helden J. Rioualen C, et al. Among authors: van helden j. Curr Protoc Bioinformatics. 2019 Jun;66(1):e72. doi: 10.1002/cpbi.72. Epub 2019 Feb 20. Curr Protoc Bioinformatics. 2019. PMID: 30786165 Free PMC article.

9

Integrative analysis of public ChIP-seq experiments reveals a complex multi-cell regulatory landscape.

Griffon A, Barbier Q, Dalino J, van Helden J, Spicuglia S, Ballester B. Griffon A, et al. Among authors: van helden j. Nucleic Acids Res. 2015 Feb 27;43(4):e27. doi: 10.1093/nar/gku1280. Epub 2014 Dec 3. Nucleic Acids Res. 2015. PMID: 25477382 Free PMC article.

10

RSAT matrix-clustering: dynamic exploration and redundancy reduction of transcription factor binding motif collections.

Castro-Mondragon JA, Jaeger S, Thieffry D, Thomas-Chollier M, van Helden J. Castro-Mondragon JA, et al. Among authors: van helden j. Nucleic Acids Res. 2017 Jul 27;45(13):e119. doi: 10.1093/nar/gkx314. Nucleic Acids Res. 2017. PMID: 28591841 Free PMC article.

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